Variant simulator; report

Node used for reconstructing ancestral genome sequence

If a (newick) phylogenetic tree file has been provided, the visualisation of the MSA used in the calculations is shown below. The two chosen groups (i.e. ‘ingroup’ / species of interest, and outgroup) are highlighted in the tree. The outgroup, used in the computation or not, is the outgroup, which together with the reference species of interest coalesce at the node of interest, from which the ancestral sequence have been extracted. Most recent common ancestor (MRCA) is highlighted in purple and labeled. The rest of the clades in the alignment are shown in lighter grey. Regardless whether a reconstructed ancestral sequence at a node, or an outgroup, has been chosen as the ancestor, the MRCA will be highlighted.

Distribution of simulated variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of simulated variants is shown across the genome of the species of interest. The grey distribution corresponds to the total amount of simulated variants, whereas the red distribution corresponds to the subset that is overlapping with a corresponding non-gap ancestral sequence. If there is no forced sub-sampling due to lack of ancestral sequence, the distribution will be fully red.

Distribution of derived variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of derived variants is shown across the genome of the species of interest. The distribution of derived variants across the genome is shown in red.

How much of the reference genome that has an available, aligned reconstructed ancestral sequence

Table 1 Fraction of refence genome that has an available aligned reconstructed ancestral sequence. The leftmost column represents the total size of the source chromosome (in base pairs), from the species of interest. The middle column represents the size (in base pairs) of the recontructed ancestral genome (or size of aligned outgroup without gaps). The rightmost column represents the fraction of the reference genome that is covered by an ancestral sequence, i.e. the fraction of the reference with a corresponding non-gap ancestral alignment.
Size of ref. genome Size of reconstructed genome Fraction covered of ref. genome
1 274 330 532 8 395 463 0.03
2 151 935 994 4 459 500 0.03
3 132 848 913 3 026 343 0.02
4 130 910 915 3 139 200 0.02
5 104 526 007 2 995 239 0.03
6 170 843 587 4 958 670 0.03
7 121 844 099 3 627 371 0.03
8 138 966 237 3 315 331 0.02
9 139 512 083 3 270 732 0.02
10 69 359 453 1 517 623 0.02
11 79 169 978 1 469 943 0.02
12 61 602 749 1 610 485 0.03
13 208 334 590 4 843 221 0.02
14 141 755 446 3 198 729 0.02
15 140 412 725 4 230 279 0.03
16 79 944 280 2 075 088 0.03
17 63 494 081 389 760 0.01
18 55 982 971 1 501 038 0.03
X 125 939 595 2 366 104 0.02

Number of simulated variants

and how many are overlapping with an available ancestral sequence

Table with corresponding data:
Table 2.
Fraction of simulated SNPs that is overlapping with a reconstructed ancestral sequence. Column explanation from left to right:
i) chromosome number
ii) the total number of simulated SNPs
iii) the number of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
iv) the fraction of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
v) the total number of derived variants.
No of sim. SNPs Number of sim. SNPs overlapping ancestral seq. Fraction of sim. SNPs overlapping ancestral seq. Number of derived variants
1 5 336 533 158 777 0.03 745 809
2 3 394 760 92 008 0.03 402 492
3 3 297 836 71 347 0.02 276 362
4 2 710 976 61 416 0.02 283 498
5 2 471 596 62 692 0.03 272 869
6 4 517 531 121 912 0.03 450 167
7 2 959 794 81 966 0.03 331 156
8 2 720 497 64 783 0.02 310 898
9 2 954 866 71 621 0.02 312 190
10 1 835 451 39 035 0.02 151 570
11 1 718 164 29 230 0.02 139 328
12 1 869 374 46 141 0.02 147 674
13 3 602 961 83 091 0.02 436 988
14 3 037 502 67 347 0.02 289 773
15 2 601 216 70 689 0.03 360 678
16 1 647 121 42 080 0.03 193 592
17 1 446 947 7 681 0.01 36 282
18 1 486 807 36 714 0.02 142 273
X 2 143 456 38 490 0.02 211 147

Types of simulated mutations

Table with corresponding data:
Table 3
Fraction of mutation types across the simulated variants with an available corresponding ancestral sequence. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions
v) the fraction of CpG site mutations
vi) the fraction of non-CpG mutations (transitions + transversions)
No. of SNPs Fraction transitions Fraction transversions Fraction CpGs Fraction non-CpGs (1-CpGs)
1 158 777 0.23 0.15 0.62 0.38
2 92 008 0.21 0.14 0.65 0.35
3 71 347 0.15 0.10 0.76 0.24
4 61 416 0.18 0.12 0.70 0.30
5 62 692 0.20 0.13 0.66 0.34
6 121 912 0.18 0.11 0.71 0.29
7 81 966 0.20 0.13 0.67 0.33
8 64 783 0.19 0.13 0.68 0.32
9 71 621 0.17 0.11 0.72 0.28
10 39 035 0.15 0.10 0.76 0.24
11 29 230 0.15 0.09 0.76 0.24
12 46 141 0.14 0.09 0.77 0.23
13 83 091 0.20 0.13 0.67 0.33
14 67 347 0.16 0.11 0.73 0.27
15 70 689 0.25 0.16 0.59 0.41
16 42 080 0.20 0.14 0.66 0.34
17 7 681 0.05 0.03 0.92 0.08
18 36 714 0.18 0.11 0.71 0.29
X 38 490 0.16 0.11 0.73 0.27

Types of derived mutations*

  • CpG mutation information is not available.

##### Table with corresponding data:

Table 4
Fraction of mutation types across the derived variants. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions.
No. of SNPs Fraction transitions Fraction transversions
1 745 809 0.61 0.39
2 402 492 0.61 0.39
3 276 362 0.61 0.39
4 283 498 0.61 0.39
5 272 869 0.61 0.39
6 450 167 0.61 0.39
7 331 156 0.61 0.39
8 310 898 0.60 0.40
9 312 190 0.60 0.40
10 151 570 0.58 0.42
11 139 328 0.59 0.41
12 147 674 0.60 0.40
13 436 988 0.62 0.38
14 289 773 0.61 0.39
15 360 678 0.62 0.38
16 193 592 0.60 0.40
17 36 282 0.60 0.40
18 142 273 0.60 0.40
X 211 147 0.61 0.39

Visualisation of gene density

and CDS overlap

Validation of simulation parameters

Number of mutations, fractions, and substitution rates. To make sure the simulation was performed as expected, the leftmost part is the calculated numbers and rates in the parameter files, including the total number of simulated variants per chromosome, based on information from the ancestor and reference species. The middle part is the (re)calculated numbers and rates based on the total number of simulated variants. The rightmost part is the (re)calculated numbers and rates within the subset with a corresponding non-gap ancestral sequence. The comparison of parameters and simulated variants is to make sure that the simulation has been perform as intended, and the comparison between total set and the subset is to make sure that the distribution is the same even if the variants are forced to be down-sampled due to the lack of an available ancestral sequence.

Comparison of numebr of mutations between log files and actual simulated files
Parameter files
Simulated variant file
Simulated variant file
(filtered for positions with a corresponding non-gap ancestral position)
Chromosome considered: 1 Chromosome considered: 1 Chromosome considered: 1
Total mut: 1042319 Total mut: 2001782 Total mut: 60924
#AC AG AT #AC AG AT #AC AG AT
73989 176788 66263 151531 343657 116514 4682 10490 3467
7.10% 16.96% 6.36% 7.57% 17.17% 5.82% 7.68% 17.22% 5.69%
#CA CG CT #CA CG CT #CA CG CT
34322 30100 139544 63740 63387 261108 1973 1909 7872
3.29% 2.89% 13.39% 3.18% 3.17% 13.04% 3.24% 3.13% 12.92%
#GA GC GT #GA GC GT #GA GC GT
140235 30148 34438 261581 63669 64082 7939 1894 1990
13.45% 2.89% 3.30% 13.07% 3.18% 3.20% 13.03% 3.11% 3.27%
#TA TC TG #TA TC TG #TA TC TG
66150 176739 73603 116313 344128 152072 3546 10608 4554
6.35% 16.96% 7.06% 5.81% 17.19% 7.60% 5.82% 17.41% 7.47%
Total CpG mut: 123877 Total CpG mut: 3334751 Total CpG mut: 97853
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
11412 9879 40533 301314 289766 1077534 8922 8369 31763
9.21% 7.97% 32.72% 9.04% 8.69% 32.31% 9.12% 8.55% 32.46%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
40736 9825 11492 1072933 289782 303422 31248 8543 9008
32.88% 7.93% 9.28% 32.17% 8.69% 9.10% 31.93% 8.73% 9.21%
Chromosome considered: 2 Chromosome considered: 2 Chromosome considered: 2
Total mut: 573466 Total mut: 3093377 Total mut: 92757
#AC AG AT #AC AG AT #AC AG AT
45175 100977 33035 231091 524544 178071 7055 16017 5267
7.88% 17.61% 5.76% 7.47% 16.96% 5.76% 7.61% 17.27% 5.68%
#CA CG CT #CA CG CT #CA CG CT
17157 18435 71360 100114 99669 411577 2962 2969 12046
2.99% 3.21% 12.44% 3.24% 3.22% 13.31% 3.19% 3.20% 12.99%
#GA GC GT #GA GC GT #GA GC GT
72234 18515 17306 411713 99737 100718 12040 2934 3025
12.60% 3.23% 3.02% 13.31% 3.22% 3.26% 12.98% 3.16% 3.26%
#TA TC TG #TA TC TG #TA TC TG
32986 100919 45367 177677 525613 232853 5339 16103 7000
5.75% 17.60% 7.91% 5.74% 16.99% 7.53% 5.76% 17.36% 7.55%
Total CpG mut: 67881 Total CpG mut: 5637916 Total CpG mut: 158028
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
5965 6250 21806 508496 490719 1821642 14294 13606 51146
8.79% 9.21% 32.12% 9.02% 8.70% 32.31% 9.05% 8.61% 32.37%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
21914 6041 5905 1813805 490823 512431 50790 13805 14387
32.28% 8.90% 8.70% 32.17% 8.71% 9.09% 32.14% 8.74% 9.10%
Chromosome considered: 3 Chromosome considered: 3 Chromosome considered: 3
Total mut: 400090 Total mut: 3851738 Total mut: 110071
#AC AG AT #AC AG AT #AC AG AT
32474 72448 22497 284974 647769 219788 8300 18793 6145
8.12% 18.11% 5.62% 7.40% 16.82% 5.71% 7.54% 17.07% 5.58%
#CA CG CT #CA CG CT #CA CG CT
11511 12906 48310 126392 125774 519380 3563 3580 14513
2.88% 3.23% 12.07% 3.28% 3.27% 13.48% 3.24% 3.25% 13.19%
#GA GC GT #GA GC GT #GA GC GT
47587 12973 11595 519834 125769 126884 14488 3505 3605
11.89% 3.24% 2.90% 13.50% 3.27% 3.29% 13.16% 3.18% 3.28%
#TA TC TG #TA TC TG #TA TC TG
22621 72255 32913 219271 648408 287495 6337 18936 8306
5.65% 18.06% 8.23% 5.69% 16.83% 7.46% 5.76% 17.20% 7.55%
Total CpG mut: 48526 Total CpG mut: 8177391 Total CpG mut: 212061
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
4337 4588 15422 737211 711314 2641591 19121 18422 68506
8.94% 9.45% 31.78% 9.02% 8.70% 32.30% 9.02% 8.69% 32.30%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
15283 4595 4301 2631762 712138 743375 68240 18509 19263
31.49% 9.47% 8.86% 32.18% 8.71% 9.09% 32.18% 8.73% 9.08%
Chromosome considered: 4 Chromosome considered: 4 Chromosome considered: 4
Total mut: 407019 Total mut: 4627671 Total mut: 128673
#AC AG AT #AC AG AT #AC AG AT
34131 75190 23566 342893 778133 264071 9698 21915 7219
8.39% 18.47% 5.79% 7.41% 16.81% 5.71% 7.54% 17.03% 5.61%
#CA CG CT #CA CG CT #CA CG CT
11332 11944 48309 151739 151298 623668 4137 4163 17054
2.78% 2.93% 11.87% 3.28% 3.27% 13.48% 3.22% 3.24% 13.25%
#GA GC GT #GA GC GT #GA GC GT
47731 11988 11198 624537 151152 152386 16924 4108 4220
11.73% 2.95% 2.75% 13.50% 3.27% 3.29% 13.15% 3.19% 3.28%
#TA TC TG #TA TC TG #TA TC TG
23441 74459 33730 263392 778988 345414 7441 22080 9714
5.76% 18.29% 8.29% 5.69% 16.83% 7.46% 5.78% 17.16% 7.55%
Total CpG mut: 41951 Total CpG mut: 10112434 Total CpG mut: 254875
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
3825 3644 13407 911461 879093 3267118 22967 22069 82469
9.12% 8.69% 31.96% 9.01% 8.69% 32.31% 9.01% 8.66% 32.36%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
13535 3720 3820 3254930 880034 919798 81982 22201 23187
32.26% 8.87% 9.11% 32.19% 8.70% 9.10% 32.17% 8.71% 9.10%
Chromosome considered: 5 Chromosome considered: 5 Chromosome considered: 5
Total mut: 385823 Total mut: 5361195 Total mut: 149711
#AC AG AT #AC AG AT #AC AG AT
30998 69425 22975 396365 899893 305514 11237 25378 8405
8.03% 17.99% 5.95% 7.39% 16.79% 5.70% 7.51% 16.95% 5.61%
#CA CG CT #CA CG CT #CA CG CT
11255 11291 48050 176021 175645 724422 4812 4832 19974
2.92% 2.93% 12.45% 3.28% 3.28% 13.51% 3.21% 3.23% 13.34%
#GA GC GT #GA GC GT #GA GC GT
47917 11093 11556 724914 175279 176890 19828 4807 4931
12.42% 2.88% 3.00% 13.52% 3.27% 3.30% 13.24% 3.21% 3.29%
#TA TC TG #TA TC TG #TA TC TG
22828 67566 30869 304836 901360 400056 8643 25591 11273
5.92% 17.51% 8.00% 5.69% 16.81% 7.46% 5.77% 17.09% 7.53%
Total CpG mut: 40249 Total CpG mut: 11850506 Total CpG mut: 296529
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
3684 3294 13044 1068675 1029701 3828347 26776 25659 95959
9.15% 8.18% 32.41% 9.02% 8.69% 32.31% 9.03% 8.65% 32.36%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
13074 3371 3782 3813747 1032131 1077905 95331 25802 27002
32.48% 8.38% 9.40% 32.18% 8.71% 9.10% 32.15% 8.70% 9.11%
Chromosome considered: 6 Chromosome considered: 6 Chromosome considered: 6
Total mut: 641932 Total mut: 6576002 Total mut: 184981
#AC AG AT #AC AG AT #AC AG AT
51837 115009 35822 482097 1094731 371686 13753 31143 10370
8.08% 17.92% 5.58% 7.33% 16.65% 5.65% 7.43% 16.84% 5.61%
#CA CG CT #CA CG CT #CA CG CT
18679 20448 79009 218825 217807 899582 6011 6038 25058
2.91% 3.19% 12.31% 3.33% 3.31% 13.68% 3.25% 3.26% 13.55%
#GA GC GT #GA GC GT #GA GC GT
78630 20524 18576 899995 217807 219726 24763 5979 6204
12.25% 3.20% 2.89% 13.69% 3.31% 3.34% 13.39% 3.23% 3.35%
#TA TC TG #TA TC TG #TA TC TG
36198 115067 52133 370836 1096385 486525 10456 31380 13826
5.64% 17.93% 8.12% 5.64% 16.67% 7.40% 5.65% 16.96% 7.47%
Total CpG mut: 79251 Total CpG mut: 15153230 Total CpG mut: 383171
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
6852 7270 25672 1366707 1317114 4894604 34574 33138 124010
8.65% 9.17% 32.39% 9.02% 8.69% 32.30% 9.02% 8.65% 32.36%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
25279 7214 6964 4876706 1320745 1377354 123286 33286 34877
31.90% 9.10% 8.79% 32.18% 8.72% 9.09% 32.18% 8.69% 9.10%
Chromosome considered: 7 Chromosome considered: 7 Chromosome considered: 7
Total mut: 472322 Total mut: 7474645 Total mut: 211857
#AC AG AT #AC AG AT #AC AG AT
37460 84882 28188 547435 1241532 421930 15688 35613 11956
7.93% 17.97% 5.97% 7.32% 16.61% 5.64% 7.40% 16.81% 5.64%
#CA CG CT #CA CG CT #CA CG CT
13542 14761 58290 249357 248344 1024662 6912 6940 28744
2.87% 3.13% 12.34% 3.34% 3.32% 13.71% 3.26% 3.28% 13.57%
#GA GC GT #GA GC GT #GA GC GT
57901 14630 14011 1026026 248139 250210 28433 6850 7094
12.26% 3.10% 2.97% 13.73% 3.32% 3.35% 13.42% 3.23% 3.35%
#TA TC TG #TA TC TG #TA TC TG
27740 83951 36966 420944 1243830 552236 11933 35839 15855
5.87% 17.77% 7.83% 5.63% 16.64% 7.39% 5.63% 16.92% 7.48%
Total CpG mut: 55073 Total CpG mut: 17214381 Total CpG mut: 438261
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
4726 4901 17826 1553055 1496647 5559223 39560 37816 141917
8.58% 8.90% 32.37% 9.02% 8.69% 32.29% 9.03% 8.63% 32.38%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
17812 4938 4870 5540093 1500451 1564912 140912 38100 39956
32.34% 8.97% 8.84% 32.18% 8.72% 9.09% 32.15% 8.69% 9.12%
Chromosome considered: 8 Chromosome considered: 8 Chromosome considered: 8
Total mut: 447494 Total mut: 8329523 Total mut: 232303
#AC AG AT #AC AG AT #AC AG AT
36470 80627 28019 612930 1389193 472481 17263 39130 13145
8.15% 18.02% 6.26% 7.36% 16.68% 5.67% 7.43% 16.84% 5.66%
#CA CG CT #CA CG CT #CA CG CT
12873 12509 52977 275970 275240 1134734 7575 7606 31365
2.88% 2.80% 11.84% 3.31% 3.30% 13.62% 3.26% 3.27% 13.50%
#GA GC GT #GA GC GT #GA GC GT
52553 12602 13076 1135625 274988 276918 31061 7471 7747
11.74% 2.82% 2.92% 13.63% 3.30% 3.32% 13.37% 3.22% 3.33%
#TA TC TG #TA TC TG #TA TC TG
27899 81047 36842 471190 1392255 617999 13166 39359 17415
6.23% 18.11% 8.23% 5.66% 16.71% 7.42% 5.67% 16.94% 7.50%
Total CpG mut: 42812 Total CpG mut: 19080000 Total CpG mut: 482598
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
3915 3624 13843 1722207 1658627 6160770 43591 41610 156128
9.14% 8.46% 32.33% 9.03% 8.69% 32.29% 9.03% 8.62% 32.35%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
13740 3714 3976 6140462 1663184 1734750 155354 41958 43957
32.09% 8.68% 9.29% 32.18% 8.72% 9.09% 32.19% 8.69% 9.11%
Chromosome considered: 9 Chromosome considered: 9 Chromosome considered: 9
Total mut: 458068 Total mut: 9203601 Total mut: 252598
#AC AG AT #AC AG AT #AC AG AT
37027 84339 27107 677909 1536992 522668 18786 42587 14275
8.08% 18.41% 5.92% 7.37% 16.70% 5.68% 7.44% 16.86% 5.65%
#CA CG CT #CA CG CT #CA CG CT
12892 14167 53555 304153 303672 1251826 8179 8274 34124
2.81% 3.09% 11.69% 3.30% 3.30% 13.60% 3.24% 3.28% 13.51%
#GA GC GT #GA GC GT #GA GC GT
54092 14174 13281 1252679 303504 305533 33753 8157 8440
11.81% 3.09% 2.90% 13.61% 3.30% 3.32% 13.36% 3.23% 3.34%
#TA TC TG #TA TC TG #TA TC TG
27223 82656 37555 521314 1539861 683490 14327 42748 18948
5.94% 18.04% 8.20% 5.66% 16.73% 7.43% 5.67% 16.92% 7.50%
Total CpG mut: 48042 Total CpG mut: 21160788 Total CpG mut: 533924
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
4296 4628 15177 1910506 1839464 6831658 48226 46009 172673
8.94% 9.63% 31.59% 9.03% 8.69% 32.28% 9.03% 8.62% 32.34%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
15093 4510 4338 6810533 1844736 1923891 172020 46342 48654
31.42% 9.39% 9.03% 32.18% 8.72% 9.09% 32.22% 8.68% 9.11%
Chromosome considered: 10 Chromosome considered: 10 Chromosome considered: 10
Total mut: 232099 Total mut: 9643727 Total mut: 262154
#AC AG AT #AC AG AT #AC AG AT
22448 43734 13416 710108 1609999 547300 19486 44230 14820
9.67% 18.84% 5.78% 7.36% 16.69% 5.68% 7.43% 16.87% 5.65%
#CA CG CT #CA CG CT #CA CG CT
5982 7216 23502 318902 318342 1312403 8481 8598 35448
2.58% 3.11% 10.13% 3.31% 3.30% 13.61% 3.24% 3.28% 13.52%
#GA GC GT #GA GC GT #GA GC GT
23246 7127 5972 1313255 318170 320345 35061 8493 8762
10.02% 3.07% 2.57% 13.62% 3.30% 3.32% 13.37% 3.24% 3.34%
#TA TC TG #TA TC TG #TA TC TG
13124 43916 22416 546222 1612723 715958 14869 44272 19634
5.65% 18.92% 9.66% 5.66% 16.72% 7.42% 5.67% 16.89% 7.49%
Total CpG mut: 22334 Total CpG mut: 22556113 Total CpG mut: 563403
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
1966 2283 6984 2036655 1960835 7282079 50855 48521 182311
8.80% 10.22% 31.27% 9.03% 8.69% 32.28% 9.03% 8.61% 32.36%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
6861 2227 2013 7259576 1966488 2050480 181496 48816 51404
30.72% 9.97% 9.01% 32.18% 8.72% 9.09% 32.21% 8.66% 9.12%
Chromosome considered: 11 Chromosome considered: 11 Chromosome considered: 11
Total mut: 204502 Total mut: 10033716 Total mut: 269186
#AC AG AT #AC AG AT #AC AG AT
18111 37573 12279 739903 1676888 570184 20001 45462 15240
8.86% 18.37% 6.00% 7.37% 16.71% 5.68% 7.43% 16.89% 5.66%
#CA CG CT #CA CG CT #CA CG CT
5889 5777 22834 331461 330734 1362826 8707 8821 36385
2.88% 2.82% 11.17% 3.30% 3.30% 13.58% 3.23% 3.28% 13.52%
#GA GC GT #GA GC GT #GA GC GT
22435 5829 5569 1363896 330611 332824 35979 8714 8996
10.97% 2.85% 2.72% 13.59% 3.30% 3.32% 13.37% 3.24% 3.34%
#TA TC TG #TA TC TG #TA TC TG
12408 37588 18210 568986 1679730 745673 15302 45452 20127
6.07% 18.38% 8.90% 5.67% 16.74% 7.43% 5.68% 16.88% 7.48%
Total CpG mut: 18763 Total CpG mut: 23884288 Total CpG mut: 585601
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
1840 1689 5923 2156021 2075920 7711645 52861 50454 189493
9.81% 9.00% 31.57% 9.03% 8.69% 32.29% 9.03% 8.62% 32.36%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
5810 1693 1808 7687622 2081937 2171143 188582 50734 53477
30.97% 9.02% 9.64% 32.19% 8.72% 9.09% 32.20% 8.66% 9.13%
Chromosome considered: 12 Chromosome considered: 12 Chromosome considered: 12
Total mut: 213568 Total mut: 10432484 Total mut: 279624
#AC AG AT #AC AG AT #AC AG AT
18882 40030 11324 767041 1738452 590683 20720 47062 15779
8.84% 18.74% 5.30% 7.35% 16.66% 5.66% 7.41% 16.83% 5.64%
#CA CG CT #CA CG CT #CA CG CT
5413 7295 23824 346327 345336 1423513 9051 9191 37911
2.53% 3.42% 11.16% 3.32% 3.31% 13.65% 3.24% 3.29% 13.56%
#GA GC GT #GA GC GT #GA GC GT
23869 7250 5300 1424422 345328 347599 37580 9097 9391
11.18% 3.39% 2.48% 13.65% 3.31% 3.33% 13.44% 3.25% 3.36%
#TA TC TG #TA TC TG #TA TC TG
11231 40065 19085 589871 1741063 772849 15868 47109 20865
5.26% 18.76% 8.94% 5.65% 16.69% 7.41% 5.67% 16.85% 7.46%
Total CpG mut: 24797 Total CpG mut: 25354894 Total CpG mut: 621304
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
2184 2538 7649 2289013 2203802 8186473 56060 53600 200984
8.81% 10.24% 30.85% 9.03% 8.69% 32.29% 9.02% 8.63% 32.35%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
7691 2636 2099 8160950 2210062 2304594 200124 53821 56715
31.02% 10.63% 8.46% 32.19% 8.72% 9.09% 32.21% 8.66% 9.13%
Chromosome considered: 13 Chromosome considered: 13 Chromosome considered: 13
Total mut: 613285 Total mut: 11610874 Total mut: 306903
#AC AG AT #AC AG AT #AC AG AT
41883 101996 38535 856202 1940617 659483 22840 51757 17440
6.83% 16.63% 6.28% 7.37% 16.71% 5.68% 7.44% 16.86% 5.68%
#CA CG CT #CA CG CT #CA CG CT
21328 17581 85681 383429 382932 1576489 9904 10082 41490
3.48% 2.87% 13.97% 3.30% 3.30% 13.58% 3.23% 3.29% 13.52%
#GA GC GT #GA GC GT #GA GC GT
85777 17710 21253 1578393 382530 384812 41121 9951 10260
13.99% 2.89% 3.47% 13.59% 3.29% 3.31% 13.40% 3.24% 3.34%
#TA TC TG #TA TC TG #TA TC TG
39169 100415 41957 658668 1943983 863336 17487 51680 22891
6.39% 16.37% 6.84% 5.67% 16.74% 7.44% 5.70% 16.84% 7.46%
Total CpG mut: 76296 Total CpG mut: 27779465 Total CpG mut: 677116
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
6993 5827 25296 2507935 2415278 8967701 61136 58418 219000
9.17% 7.64% 33.16% 9.03% 8.69% 32.28% 9.03% 8.63% 32.34%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
25152 5918 7110 8942297 2420972 2525282 218111 58747 61704
32.97% 7.76% 9.32% 32.19% 8.71% 9.09% 32.21% 8.68% 9.11%
Chromosome considered: 14 Chromosome considered: 14 Chromosome considered: 14
Total mut: 409379 Total mut: 12394286 Total mut: 324754
#AC AG AT #AC AG AT #AC AG AT
31775 70825 23678 913116 2068648 702906 24175 54643 18420
7.76% 17.30% 5.78% 7.37% 16.69% 5.67% 7.44% 16.83% 5.67%
#CA CG CT #CA CG CT #CA CG CT
12705 13297 53125 410012 409703 1686340 10513 10671 43935
3.10% 3.25% 12.98% 3.31% 3.31% 13.61% 3.24% 3.29% 13.53%
#GA GC GT #GA GC GT #GA GC GT
52979 13080 12885 1688108 408829 411856 43517 10642 10861
12.94% 3.20% 3.15% 13.62% 3.30% 3.32% 13.40% 3.28% 3.34%
#TA TC TG #TA TC TG #TA TC TG
23322 70102 31606 701933 2072564 920271 18510 54625 24242
5.70% 17.12% 7.72% 5.66% 16.72% 7.42% 5.70% 16.82% 7.46%
Total CpG mut: 58110 Total CpG mut: 30033555 Total CpG mut: 726612
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
5214 5065 18728 2711438 2611095 9695341 65560 62741 234863
8.97% 8.72% 32.23% 9.03% 8.69% 32.28% 9.02% 8.63% 32.32%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
18866 5100 5137 9668293 2617471 2729917 234168 63172 66108
32.47% 8.78% 8.84% 32.19% 8.72% 9.09% 32.23% 8.69% 9.10%
Chromosome considered: 15 Chromosome considered: 15 Chromosome considered: 15
Total mut: 500470 Total mut: 13352389 Total mut: 353573
#AC AG AT #AC AG AT #AC AG AT
34365 84799 32724 986257 2233774 758746 26393 59811 20223
6.87% 16.94% 6.54% 7.39% 16.73% 5.68% 7.46% 16.92% 5.72%
#CA CG CT #CA CG CT #CA CG CT
17247 13195 68269 439944 439765 1810550 11345 11552 47581
3.45% 2.64% 13.64% 3.29% 3.29% 13.56% 3.21% 3.27% 13.46%
#GA GC GT #GA GC GT #GA GC GT
68333 13299 16926 1812495 439071 442118 47127 11522 11673
13.65% 2.66% 3.38% 13.57% 3.29% 3.31% 13.33% 3.26% 3.30%
#TA TC TG #TA TC TG #TA TC TG
32406 84222 34685 757897 2238264 993508 20222 59658 26466
6.48% 16.83% 6.93% 5.68% 16.76% 7.44% 5.72% 16.87% 7.49%
Total CpG mut: 55272 Total CpG mut: 31676668 Total CpG mut: 768482
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
5246 3997 18313 2860365 2753903 10225091 69260 66448 248354
9.49% 7.23% 33.13% 9.03% 8.69% 32.28% 9.01% 8.65% 32.32%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
18278 4066 5372 10197615 2760166 2879528 247678 66793 69949
33.07% 7.36% 9.72% 32.19% 8.71% 9.09% 32.23% 8.69% 9.10%
Chromosome considered: 16 Chromosome considered: 16 Chromosome considered: 16
Total mut: 286393 Total mut: 13899900 Total mut: 367830
#AC AG AT #AC AG AT #AC AG AT
21826 51047 18333 1028192 2328106 790678 27499 62298 21064
7.62% 17.82% 6.40% 7.40% 16.75% 5.69% 7.48% 16.94% 5.73%
#CA CG CT #CA CG CT #CA CG CT
8689 8734 34595 457340 457198 1882300 11814 12006 49383
3.03% 3.05% 12.08% 3.29% 3.29% 13.54% 3.21% 3.26% 13.43%
#GA GC GT #GA GC GT #GA GC GT
34591 8707 8596 1883540 456351 459401 48900 11957 12158
12.08% 3.04% 3.00% 13.55% 3.28% 3.31% 13.29% 3.25% 3.31%
#TA TC TG #TA TC TG #TA TC TG
17980 51279 22016 789751 2331868 1035175 21083 62122 27546
6.28% 17.91% 7.69% 5.68% 16.78% 7.45% 5.73% 16.89% 7.49%
Total CpG mut: 31548 Total CpG mut: 32776278 Total CpG mut: 796305
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
2878 2726 9968 2960455 2849947 10579279 71814 68840 257359
9.12% 8.64% 31.60% 9.03% 8.70% 32.28% 9.02% 8.64% 32.32%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
10227 2905 2844 10551320 2856137 2979140 256660 69139 72493
32.42% 9.21% 9.01% 32.19% 8.71% 9.09% 32.23% 8.68% 9.10%
Chromosome considered: 17 Chromosome considered: 17 Chromosome considered: 17
Total mut: 51892 Total mut: 13997627 Total mut: 368429
#AC AG AT #AC AG AT #AC AG AT
3913 9348 3200 1035125 2343916 795878 27543 62388 21092
7.54% 18.01% 6.17% 7.40% 16.75% 5.69% 7.48% 16.93% 5.72%
#CA CG CT #CA CG CT #CA CG CT
1598 1668 6310 460779 460727 1896525 11835 12033 49477
3.08% 3.21% 12.16% 3.29% 3.29% 13.55% 3.21% 3.27% 13.43%
#GA GC GT #GA GC GT #GA GC GT
6389 1649 1784 1897540 459756 462824 48985 11973 12181
12.31% 3.18% 3.44% 13.56% 3.28% 3.31% 13.30% 3.25% 3.31%
#TA TC TG #TA TC TG #TA TC TG
3141 8904 3988 795115 2347344 1042098 21130 62212 27580
6.05% 17.16% 7.69% 5.68% 16.77% 7.44% 5.74% 16.89% 7.49%
Total CpG mut: 6909 Total CpG mut: 34125498 Total CpG mut: 803387
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
611 605 2178 3081749 2966704 11015473 72462 69426 259615
8.84% 8.76% 31.52% 9.03% 8.69% 32.28% 9.02% 8.64% 32.32%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
2168 667 680 10985792 2973808 3101972 258985 69756 73143
31.38% 9.65% 9.84% 32.19% 8.71% 9.09% 32.24% 8.68% 9.10%
Chromosome considered: 18 Chromosome considered: 18 Chromosome considered: 18
Total mut: 210913 Total mut: 14396631 Total mut: 379218
#AC AG AT #AC AG AT #AC AG AT
18674 40528 12451 1064197 2409818 818261 28332 64234 21668
8.85% 19.22% 5.90% 7.39% 16.74% 5.68% 7.47% 16.94% 5.71%
#CA CG CT #CA CG CT #CA CG CT
5284 6473 22269 474241 474501 1951923 12202 12394 50976
2.51% 3.07% 10.56% 3.29% 3.30% 13.56% 3.22% 3.27% 13.44%
#GA GC GT #GA GC GT #GA GC GT
21892 6380 5285 1952499 473175 476406 50442 12321 12511
10.38% 3.02% 2.51% 13.56% 3.29% 3.31% 13.30% 3.25% 3.30%
#TA TC TG #TA TC TG #TA TC TG
12370 40717 18590 817313 2413006 1071291 21717 64042 28379
5.86% 19.31% 8.81% 5.68% 16.76% 7.44% 5.73% 16.89% 7.48%
Total CpG mut: 20470 Total CpG mut: 35213301 Total CpG mut: 829312
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
1801 2170 6332 3180103 3060920 11366705 74783 71678 267976
8.80% 10.60% 30.93% 9.03% 8.69% 32.28% 9.02% 8.64% 32.31%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
6249 2096 1822 11336182 3068779 3200612 267342 72044 75489
30.53% 10.24% 8.90% 32.19% 8.71% 9.09% 32.24% 8.69% 9.10%
Chromosome considered: X Chromosome considered: X Chromosome considered: X
Total mut: 291732 Total mut: 14953208 Total mut: 389540
#AC AG AT #AC AG AT #AC AG AT
21970 51186 17872 1106310 2505154 850800 29105 65921 22263
7.53% 17.55% 6.13% 7.40% 16.75% 5.69% 7.47% 16.92% 5.72%
#CA CG CT #CA CG CT #CA CG CT
9553 9043 36312 491949 492157 2024859 12539 12714 52355
3.27% 3.10% 12.45% 3.29% 3.29% 13.54% 3.22% 3.26% 13.44%
#GA GC GT #GA GC GT #GA GC GT
36349 8838 9273 2025726 490965 494054 51805 12661 12845
12.46% 3.03% 3.18% 13.55% 3.28% 3.30% 13.30% 3.25% 3.30%
#TA TC TG #TA TC TG #TA TC TG
17888 51843 21605 849626 2508378 1113230 22320 65854 29158
6.13% 17.77% 7.41% 5.68% 16.77% 7.44% 5.73% 16.91% 7.49%
Total CpG mut: 30513 Total CpG mut: 36800180 Total CpG mut: 857480
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
2808 2515 9897 3322848 3199002 11878914 77372 74130 276981
9.20% 8.24% 32.44% 9.03% 8.69% 32.28% 9.02% 8.65% 32.30%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
9887 2543 2863 11847080 3207483 3344853 276465 74515 78017
32.40% 8.33% 9.38% 32.19% 8.72% 9.09% 32.24% 8.69% 9.10%